Probing the Unique Dehydration-Induced Structural Modifications in Cancer Cell DNA Using Surface Enhanced Raman Spectroscopy

SERS microscopy as a tool for comprehensive biochemical characterization in complex samples

Surface enhanced Raman scattering (SERS) spectra of biomaterials such as cells or tissues can be used to obtain biochemical information from nanoscopic volumes in these heterogeneous samples. This tutorial review discusses the factors that determine the outcome of a SERS experiment in complex bioorganic samples. They are related to the SERS process itself, the possibility to selectively probe certain regions or constituents of a sample, and the retrieval of the vibrational information in order to identify molecules and their interaction. After introducing basic aspects of SERS experiments in the context of biocompatible environments, spectroscopy in typical microscopic settings is exemplified, including the possibilities to combine SERS with other linear and non-linear microscopic tools, and to exploit approaches that improve lateral and temporal resolution. In particular the great variation of data in a SERS experiment calls for robust data analysis tools. Approaches will be introduced that have been originally developed in the field of bioinformatics for the application to omics data and that show specific potential in the analysis of SERS data. They include the use of simulated data and machine learning tools that can yield chemical information beyond achieving spectral classification.

On-chip dielectrophoretic device for cancer cell manipulation: A numerical and artificial neural network study

Breast cancer, as one of the most frequent types of cancer in women, imposes large financial and human losses annually. MCF-7, a well-known cell line isolated from the breast tissue of cancer patients, is usually used in breast cancer research. Microfluidics is a newly established technique that provides many benefits, such as sample volume reduction, high-resolution operations, and multiple parallel analyses for various cell studies. This numerical study presents a novel microfluidic chip for the separation of MCF-7 cells from other blood cells, considering the effect of dielectrophoretic force. An artificial neural network, a novel tool for pattern recognition and data prediction, is implemented in this research. To prevent hyperthermia in cells, the temperature should not exceed 35 °C. In the first part, the effect of flow rate and applied voltage on the separation time, focusing efficiency, and maximum temperature of the field is investigated. The results denote that the separation time is affected by both the input parameters inversely, whereas the two remaining parameters increase with the input voltage and decrease with the sheath flow rate. A maximum focusing efficiency of 81% is achieved with a purity of 100% for a flow rate of 0.2 μ L / min and a voltage of 3.1 V . In the second part, an artificial neural network model is established to predict the maximum temperature inside the separation microchannel with a relative error of less than 3% for a wide range of input parameters. Therefore, the suggested label-free lab-on-a-chip device separates the target cells with high-throughput and low voltages.

Lifting the Veil: Characteristics, Clinical Significance, and Application of β-2-Microglobulin as Biomarkers and Its Detection with Biosensors

Because β-2-microglobulin (β₂M) is a surface protein that is present on most nucleated cells, it plays a key role in the human immune system and the kidney glomeruli to regulate homeostasis. The primary clinical significance of β₂M is in dialysis-related amyloidosis, a complication of end-stage renal disease caused by a gradual accumulation of β₂M in the blood. Therefore, the function of β₂M in kidney-related diseases has been extensively studied to evaluate its glomerular and tubular functions. Because increased β₂M shedding due to rapid cell turnover may indicate other underlying medical conditions, the possibility to use β₂M as a versatile biomarker rose in prominence across multiple disciplines for various applications. Therefore, this work has reviewed the recent use of β₂M to detect various diseases and its progress as a biomarker. While the use of state-of-the-art β₂M detection requires sophisticated tools, high maintenance, and labor cost, this work also has reported the use of biosensor to quantify β₂M over the past decade. It is hoped that a portable and highly efficient β₂M biosensor device will soon be incorporated in point-of-care testing to provide safe, rapid, and reliable test results.

Discrimination of Receptor-Mediated Endocytosis by Surface-Enhanced Raman Scattering

Cellular energy required for the maintenance of cellular life is stored in the form of adenosine triphosphate (ATP). Understanding cellular mechanisms, including ATP-dependent metabolisms, is crucial for disease diagnosis and treatment, including drug development and investigation of new therapeutic systems. As an ATP-dependent metabolism, endocytosis plays a key role not only in the internalization of molecules but also in processes including cell growth, differentiation, and signaling. To understand cellular mechanisms including endocytosis, many techniques ranging from molecular approaches to spectroscopy are used. Surface-enhanced Raman scattering (SERS) is shown to provide valuable label-free molecular information from living cells. In this study, receptor-mediated endocytosis was investigated with SERS by inhibiting endocytosis with ATP depletion agents: sodium azide (NaN₃) and 2-deoxy-d-glucose (dG). Human lung bronchial epithelium (Beas-2b) cells, normal prostate epithelium (PNT1A) cells, and cervical cancer epithelium (HeLa) cells were used as models. First, the effect of NaN₃ and dG on the cells were examined through cytotoxicity, apoptosis-necrosis, ATP assay, and uptake inhibition analysis. An attempt to relate the spectral changes in the cellular spectra to the studied cellular events, receptor-mediated endocytosis inhibition, was made. It was found that the effect of two different ATP depletion agents can be discriminated by SERS, and hence receptor-mediated endocytosis can be tracked from single living cells with the technique without using a label and with limited sample preparation.

Surface enhanced Raman scattering for probing cellular biochemistry

Surface enhanced Raman scattering (SERS) from biomolecules in living cells enables the sensitive, but also very selective, probing of their biochemical composition. This minireview discusses the developments of SERS probing in cells over the past years from the proof-of-principle to observe a biochemical status to the characterization of molecule-nanostructure and molecule-molecule interactions and cellular processes that involve a wide variety of biomolecules and cellular compartments. Progress in applying SERS as a bioanalytical tool in living cells, to gain a better understanding of cellular physiology and to harness the selectivity of SERS, has been achieved by a combination of live cell SERS with several different approaches. They range from organelle targeting, spectroscopy of relevant molecular models, and the optimization of plasmonic nanostructures to the application of machine learning and help us to unify the information from defined biomolecules and from the cell as an extremely complex system.

Cancer Stem Cell DNA Enabled Real-Time Genotyping with Self-Functionalized Quantum Superstructures-Overcoming the Barriers of Noninvasive cfDNA Cancer Diagnostics

Cancer diagnosis and determining its tissue of origin are crucial for clinical implementation of personalized medicine. Conventional diagnostic techniques such as imaging and tissue biopsy are unable to capture the dynamic tumor landscape. Although circulating tumor DNA (ctDNA) shows promise for diagnosis, the clinical relevance of ctDNA remains largely undetermined due to several biological and technical complexities. Here, cancer stem cell-ctDNA is used to overcome the biological complexities like the inability for molecular analysis of ctDNA and dependence on ctDNA concentration rather than the molecular profile. Ultrasensitive quantum superstructures overcome the technical complexities of trace-level detection and rapid diagnosis to detect ctDNA within its short half-life. Activation of multiple surface enhanced Raman scattering mechanisms of the quantum superstructures achieved a very high enhancement factor (1.35 × 10¹¹ ) and detection at ultralow concentration (10^-15 M) with very high reliability (RSD: 3-12%). Pilot validation with clinical plasma samples from an independent validation cohort achieved a diagnosis sensitivity of ≈95% and specificity of 83%. Quantum superstructures identified the tissue of origin with ≈75-86% sensitivity and ≈92-96% specificity. With large scale clinical validation, the technology can develop into a clinically useful liquid biopsy tool improving cancer diagnostics.

Raman Spectroscopy: A Potential Diagnostic Tool for Oral Diseases

Oral diseases impose a major health burden worldwide and have a profound effect on general health. Dental caries, periodontal diseases, and oral cancers are the most common oral health conditions. Their occurrence and development are related to oral microbes, and effective measures for their prevention and the promotion of oral health are urgently needed. Raman spectroscopy detects molecular vibration information by collecting inelastic scattering light, allowing a “fingerprint” of a sample to be acquired. It provides the advantages of rapid, sensitive, accurate, and minimally invasive detection as well as minimal interference from water in the “fingerprint region.” Owing to these characteristics, Raman spectroscopy has been used in medical detection in various fields to assist diagnosis and evaluate prognosis, such as detecting and differentiating between bacteria or between neoplastic and normal brain tissues. Many oral diseases are related to oral microbial dysbiosis, and their lesions differ from normal tissues in essential components. The colonization of keystone pathogens, such as Porphyromonas gingivalis, resulting in microbial dysbiosis in subgingival plaque, is the main cause of periodontitis. Moreover, the components in gingival crevicular fluid, such as infiltrating inflammatory cells and tissue degradation products, are markedly different between individuals with and without periodontitis. Regarding dental caries, the compositions of decayed teeth are transformed, accompanied by an increase in acid-producing bacteria. In oral cancers, the compositions and structures of lesions and normal tissues are different. Thus, the changes in bacteria and the components of saliva and tissue can be used in examinations as special markers for these oral diseases, and Raman spectroscopy has been acknowledged as a promising measure for detecting these markers. This review summarizes and discusses key research and remaining problems in this area. Based on this, suggestions for further study are proposed.

Broadband SERS Enhancement by DNA Origami Assembled Bimetallic Nanoantennas with Label-Free Single Protein Sensing

Engineering hotspots in surface-enhanced Raman spectroscopy (SERS) through precisely controlled assembly of plasmonic nanostructures capable of expanding intense field enhancement are highly desirable to enhance the potentiality of SERS as a label-free optical tool for single molecule detection. Inspired by DNA origami technique, we constructed plasmonic dimer nanoantennas with a tunable gap decorated with Ag-coated Au nanostars on origami. Herein, we demonstrate the single-molecule SERS enhancements of three dyes with emission in different spectral regions after incorporation of single dye molecules in between two nanostars. The enhancement factors (EFs) achieved in the range of 10⁹-10¹⁰ for all the single dye molecules, under both resonant and nonresonant excitation conditions, would enable enhanced photostability during time-series measurement. We further successfully explored the potential of our designed nanoantennas to accommodate and detect a single thrombin protein molecule after selective placement in the wide nanogap of 10 nm. Our results suggest that such nanoantennas can serve as a broadband SERS enhancer and enable specific detection of target biological molecules with single-molecule sensitivity.

Raman Mapping of Biological Systems Interacting with a Disordered Nanostructured Surface: A Simple and Powerful Approach to the Label-Free Analysis of Single DNA Bases

This article demonstrates the possibility to use a novel powerful approach based on Raman mapping of analyte solutions drop casted on a disordered array of Ag covered silicon nanowires (Ag/SiNWs), to identify the characteristic spectral signal of the four DNA bases, adenine (A), thymine (T), cytosine (C), and guanine (G), at concentration as low as 10 ng/µL, and to study their specific way of interacting with the nanostructured substrate. The results show a distinctive and amplified interaction of guanine, the base that is most susceptible to oxidation, with the nanostructured surface. Our findings explain the recently revealed diverse behaviour of cancer and normal DNA deposited on the same Ag/SiNWs, which is ascribed to mechanical deformation and base lesions present on the oxidised DNA molecule backbone and causes detectable variation in the Raman signal, usable for diagnostic purposes. The notable bio-analytical capability of the presented platform, and its sensitivity to the molecule mechanical conformation at the single-base level, thus provides a new reliable, rapid, label-free DNA diagnostic methodology alternative to more sophisticated and expensive sequencing ones.

Silver-coated silicon nanowire platform discriminates genomic DNA from normal and malignant human epithelial cells using label-free Raman spectroscopy

Genomic deoxyribonucleic acid (DNA) stores and carries the information required to maintain and replicate cellular life. While much efforts have been devoted in decoding the sequence of DNA basis to detect the genetic mutations related to cancer disease, it is becoming clear that physical properties, like structural conformation, stiffness and shape, can play an important role to recognize DNA modifications. Here, silver-coated silicon nanowires (Ag/SiNWs) are exploited as Raman spectroscopic platform to easily discriminate healthy and cancer genomic DNA, extracted from human normal skin and malignant melanoma cells, respectively. In particular, aqueous DNA droplets are directly deposited onto a forest of Ag/SiNWs and Raman maps are acquired after sample dehydration. By applying principal component analysis (PCA) to the Raman spectra collected within the droplets, healthy and cancer cell DNA can be distinguished without false negative identifications and with few false positive results (< 2%). The discrimination occurs regardless the analysis of specific DNA sequencing, but through Raman bands strictly related to the interfacing of the DNA and the NWs. The observed phenomenon can be ascribed to conformational differences and/or diverse charge properties between healthy and cancer cell DNA determining a different arrangement of the molecules adsorbed onto the NWs upon water evaporation. The unique interaction with DNA and facile fabrication technology make Ag/SiNWs an effective platform for a robust, rapid and label-free cancer diagnosis, as well as a potential tool to investigate physical properties of DNA.

Plasmonic gap-enhanced Raman tag nanorods for imaging 3D pancreatic spheroids using surface-enhanced Raman spectroscopy and darkfield microscopy

Plasmonic gap-enhanced Raman tags (GERTs) are new emerging nanoprobes that, based on their unique surface-enhanced Raman spectroscopy (SERS) signal, can play a major role in complex imaging and detection of biological systems. GERTs are generated from a metal core nanostructure and layered with one or more metal nanosized layers, encasing a Raman active molecule. The advantages of GERTs are enhanced surface plasmon and electromagnetic resonance, as well as inherent protection of the Raman active molecule from environmental deterioration that could reduce their spectroscopic signatures over time. In this study, we used in vitro three-dimensional (3D) spheroid cultures to demonstrate these advantages. 3D spheroids mimic the in vivo tumor microenvironment better than 2D culture, with abundant extracellular matrix and hypoxia inducing variability of pH and enzymatic reactions. Here, we report the use of GERTs in large pancreatic 3D spheroids (>500 μm in apparent diameter) for complex penetration visualization. Our combined imaging technique of enhanced darkfield microscopy and SERS was able to identify the presence and distribution of the GERTs within the 3D spheroid structure. The distribution of GERTs 2 hours after the nanorods' incubation indicated accumulation, generally in the outermost layer of the spheroids but also, more randomly, in non-uniform patterns in deep layers of the 3D spheroids. These observations bring into question the mechanism of uptake and flow of the nanoparticles in function of their incubation time while demonstrating the promising potential of our approach. Additionally, the SERS signal was still detectable after 24 hours of incubation of GERTs with the 3D culture, indicating the stability of the Raman signal.

Plasmonic SERS Au Nanosunflowers for Sensitive and Label-Free Diagnosis of DNA Base Damage in Stimulus-Induced Cell Apoptosis

Molecular diagnosis and accurate damage analysis of complex genomic DNAs in tumor cells are crucial to the theranostics of cancers but still a huge challenge. Herein, by designed preparation of a uniform plasmonic sunflower-like assembly gold (Au) nanostructure that is capable of efficient DNA capture and providing high-density gap-plasmon "hot spots" for adequate surface-enhanced Raman spectroscopy (SERS) enhancement, we succeeded in sensitive and reliable label-free SERS detection of DNA damage in electrostimulus-induced apoptotic cancer cells at the DNA base level for the first time. The SERS results showed that the external electrostimulus (at 1.2 V, for 5 min) was almost harmless to normal healthy cells, but it caused pronounced double strand break and adenine base damage in cancer cell DNAs, which effectively destroyed the reproduction and transcription of DNAs and ultimately induced cell apoptosis. The developed sensing platform and method are promising for cell study of genetically related diseases.

Study on the precise mechanism of Mitoxantrone-induced Jurkat cell apoptosis using surface enhanced Raman scattering

Mitoxantrone (MTX), one representative of anthraquinone ring anticancer drugs, reveals excellent anticancer effects in acute leukemia. Though current studies have shown that MTX-induced acute leukemia cell apoptosis is implemented by inserting into DNA, and then leading to DNA breakage and the subsequent transcription termination, but the specific location information of MTX embedded in DNA remains unknown. In this study, combining surface enhanced Raman scattering (SERS) and principal component analysis (PCA), we achieve the biochemical changes of MTX-induced Jurkat cell apoptosis and the location information of MTX embedded in DNA. In contrast, we also present the corresponding result of Daunorubicin (DNR)-induced Jurkat cell apoptosis. It is found that the location of MTX embedded in DNA of Jurkat cell is different from DNR, in which the action site of MTX is mainly implemented by blocking and destroying AT base pairs while DNR is performed by embedding and destroying GC base pairs and then the base A. Clearly, this achieved information is very useful for the designing and modification of anthraquinone ring anticancer drugs.

Present and Future of Surface-Enhanced Raman Scattering

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

Label-free liquid biopsy based on blood circulating DNA detection using SERS-based nanotechnology for nasopharyngeal cancer screening

Development of a sensitive, rapid and easy-to-use liquid biopsy method is of imperative clinical value for point-of-care caner diagnostics. Here, a label-free and modification-free nanotechnology based on surface-enhanced Raman spectroscopy (SERS) was employed for DNA analysis. Using the SERS signals of phosphate backbone as internal standard, quantitative detection for nucleobases was achieved even at single base level. The method combined with principal component analysis and linear discriminant analysis was further applied for real blood circulating DNA detection for the first time, and an ideal diagnostic sensitivity of 83.3% and specificity of 82.5% could be obtained for differentiating the nasopharyngeal cancer from the normal group, demonstrating promising potential as an alternative nanotechnology for nasopharyngeal cancer screening based on liquid biopsy.

Single-Step FRET-Based Detection of Femtomoles DNA

Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), we show that these sensors can be regenerated in situ, and they allow detection of femtomoles DNA without the need for target amplification while still using a dramatically small sample size (fewer than three orders of magnitude compared to the typical sample size of bulk fluorescence). In addition, these single-molecule sensors exhibit a dynamic range of approximately two orders of magnitude. Using one of the sensors, we demonstrate that the single-base mismatch sequence can be discriminated from a fully matched DNA target, showing a high specificity of the method. These sensors with simple and recyclable design, sensitive detection of DNA, and the ability to discriminate single-base mismatch sequences may find applications in quantitative analysis of nucleic acid biomarkers.

Novel Surface-Enhanced Raman Spectroscopy Techniques for DNA, Protein and Drug Detection

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique in which the Raman scattering signal strength of molecules, absorbed by rough metals or the surface of nanoparticles, experiences an exponential growth (10³-10⁶ times and even 10¹⁴-10¹⁵ times) because of electromagnetic or chemical enhancements. Nowadays, SERS has attracted tremendous attention in the field of analytical chemistry due to its specific advantages, including high selectivity, rich informative spectral properties, nondestructive testing, and the prominent multiplexing capabilities of Raman spectroscopy. In this review, we present the applications of state-of-the-art SERS for the detection of DNA, proteins and drugs. Moreover, we focus on highlighting the merits and mechanisms of achieving enhanced SERS signals for food safety and clinical treatment. The machine learning techniques, combined with SERS detection, are also indicated herein. This review concludes with recommendations for future studies on the development of SERS.

Identification and Analysis of Exosomes by Surface-Enhanced Raman Spectroscopy

The concept of liquid biopsy has emerged as a novel approach for cancer screening, which is based on the analysis of circulating cancer biomarkers in body fluids. Among the various circulating cancer biomarkers, including Food and Drug Administration (FDA)-approved circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), exosomes have attracted tremendous attention due to their ability to diagnose cancer in its early stages with high efficiency. Recently, surface-enhanced Raman spectroscopy (SERS) has been applied for the detection of cancer exosomes due to its high sensitivity, specificity, and multiplexing capability. In this article, we review recent progress in the development of SERS-based technologies for in vitro identification of circulating cancer exosomes. The accent is made on the detection strategies and interpretation of the SERS data. The problems of detecting cancer-derived exosomes from patient samples and future perspectives of SERS-based diagnostics are also discussed.

Enzyme-Driven Switchable Fluorescence-SERS Diagnostic Nanococktail for the Multiplex Detection of Lung Cancer Biomarkers

Comprehensive profiling of multiple protein targets plays a critical role in deeper understanding of specific disease conditions associated with high heterogeneity and complexity. Herein, we present the design and fabrication of smart programmable nanoarchitectures, which could integrate clinically relevant diagnostic modalities for the multiplexed detection of most prevalent panel of disease biomarkers present in lung cancer. The multiplex nanoprobes were prepared by attaching dual-functional Raman-active fluorogens onto spherical gold nanoparticles through a peptide linker, Phe-Lys-Cys (FKC), which is engineered with a cathepsin B (cathB) enzyme cleavage site. The presence of cathB induces the scission of FKC upon homing into the cancer cells, resulting in the release of the initially latent fluorophores with a concomitant quenching of the surface-enhanced Raman signal intensity, thereby realizing an on-off switching between the fluorescence and Raman modalities. The enzyme-triggered switchable nanoprobes were utilized for the simultaneous detection of pathologically relevant lung cancer targets by tethering with specific antibody units. The multiplex-targeted multicolor coded detection capability of the antitags was successfully developed as a valid protein screening methodology, which can address the unmet challenges in the conventional clinical scenario for the precise and early diagnosis of lung cancer.

para-Aminothiophenol Radical Reaction-Functionalized Gold Nanoprobe for One-to-All Detection of Five Reactive Oxygen Species In Vivo

Five major reactive oxygen species (ROS) are generated in diseases including H₂O₂, ^•OH, O₂^•-, ROO^•, and ¹O₂. Simultaneous detection of the five ROS with a single probe is crucial for a comprehensive understanding of the development and progression of many diseases, such as cancer and inflammatory diseases. However, currently reported detection systems are limited by targeting one ROS with one probe. This one-to-one detection mode may fail to sufficiently unveil the diseased state. In this study, we achieved simultaneous detection of all the five ROS with one probe (i.e., one-to-all detection), by designing a novel para-aminothiophenol (PATP) and hemin-decorated gold (Au/PATP/Hemin) nanoprobe. The design is principled by our discovery that PATP can react with ^•OH, O₂^•-, ROO^•, and ¹O₂ by a radical oxidative coupling mechanism to form 4,4'-dimercaptoazobenzene (DMAB). The DMAB then elicited strong characteristic surface-enhanced Raman scattering (SERS) peaks at 1142, 1386, and 1432 cm^-1; which in turn enables direct detection of ^•OH, O₂^•-, ROO^•, and ¹O₂ and indirect detection of H₂O₂ by hemin-catalyzed fenton reaction to convert H₂O₂ into ^•OH. In two representative ROS-elevated mice models of tumors and allergic dermatitis, the Au/PATP/Hemin nanoprobe demonstrated its robust performance of monitoring tumor development and inflammation progression in a highly sensitive and quantitative manner.

Real-time tracking of the autophagy process in living cells using plasmonically enhanced Raman spectroscopy of fucoidan-coated gold nanoparticles

To date, a variety of biological assays such as immunostaining, western blotting, enzyme-linked immunosorbent assay (ELISA), and flow cytometry have been used to analyze and trace important biological events and therapies. In addition to these techniques, the application of microscopic analytical techniques such as matrix-assisted laser desorption/ionization-time of flight (MALDI-ToF) mass spectrometry and Raman spectroscopy is increasing, allowing information to be obtained at the molecular level. In this study, we have conducted real-time tracking of autophagy, a cellular process that has recently been attracting significant attention. To achieve this purpose, we performed Raman spectroscopy on human oral squamous carcinoma cells (HSC3) incubated with bioactive molecule-modified plasmonic gold nanoparticles. The bioactive molecule-nanoparticle complexes were synthesized using fucoidan, a biopolymer that induces autophagy. By using this platform, it was possible to trace the entire autophagic process successively from cell introduction to autophagic apoptosis. This fusion of nanocomposites and spectroscopic techniques is expected to enable more complex biological processes to be pursued at the molecular level in the future.

Dielectrophoresis-based microfluidic platforms for cancer diagnostics

The recent advancement of dielectrophoresis (DEP)-enabled microfluidic platforms is opening new opportunities for potential use in cancer disease diagnostics. DEP is advantageous because of its specificity, low cost, small sample volume requirement, and tuneable property for microfluidic platforms. These intrinsic advantages have made it especially suitable for developing microfluidic cancer diagnostic platforms. This review focuses on a comprehensive analysis of the recent developments of DEP enabled microfluidic platforms sorted according to the target cancer cell. Each study is critically analyzed, and the features of each platform, the performance, added functionality for clinical use, and the types of samples, used are discussed. We address the novelty of the techniques, strategies, and design configuration used in improving on existing technologies or previous studies. A summary of comparing the developmental extent of each study is made, and we conclude with a treatment of future trends and a brief summary.

Direct surface-enhanced Raman scattering (SERS) spectroscopy of nucleic acids: from fundamental studies to real-life applications

In this tutorial review, we summarize and discuss the most recent cutting-edge research in the field of direct surface-enhanced Raman scattering (SERS) analysis of nucleic acids.

SERS and SERRS Detection of the DNA Lesion 8-Nitroguanine: A Self-Labeling Modification

Rapid and sensitive methods to detect DNA lesions are essential in order to understand their role in carcinogenesis and for potential diagnosis of cancers. The 8-nitroguanine DNA lesion, which is closely associated with inflammation-induced cancers, has been characterized for the first time by surface-enhanced Raman spectroscopy (SERS). This lesion has been studied as the free base, as well as part of a dinucleotide and oligodeoxynucleotides (ODNs) at 5 different excitation wavelengths in the range 785-488 nm. All nitrated samples produced distinctly different spectra from their control guanine counterparts, with nitro bands being assigned by DFT calculations. Additional resonance enhancement was observed at the shorter excitation wavelengths, these SERRS measurements allowed the detection of one nitrated guanine in over 1,300 bases. In addition, SER(R)S can be used to detect whether the unstable lesion is covalently attached to the ODN or has been released by hydrolytic depurination.

Detection of EGFR mutation in plasma using multiplex allele-specific PCR (MAS-PCR) and surface enhanced Raman spectroscopy

In this study, surface enhanced Raman spectroscopy (SERS) in combination with multiplexed polymerase chain reaction (PCR) was utilized to detect mutations of exons 19 and 21 of the epidermal growth factor receptor (EGFR) gene. Through the use of multiplexed PCR, the two mutation types were amplified in a single reaction. SERS was used on the PCR products to detect mutations. DNA mixtures with increasing mutation percentages showed good linear relationship between mutation rates and peak height. Then, this PCR-SERS method was used on the plasma of 48 patients with non-small cell lung cancer (NSCLC) to detect EGFR mutations. Analysis of variance (ANOVA) and receiver operating characteristic (ROC) analysis revealed that the peak height ratios were significant for identifying different mutation types. The specificity, sensitivity and accuracy obtained were all 100%. The proposed method was then validated through comparison with high resolution melting (HRM) and showed high concordance with HRM (Pearson correlation is 0.92). Finally, logistic regression was performed on EGFR mutation status and the clinical features of the 48 patients. Our study indicates that PCR-SERS is an effective, noninvasive, and economical method for the detection and monitoring of EGFR mutations in the plasma of patients with NSCLC.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Detection of Genomic DNA Damage from Radiated Nasopharyngeal Carcinoma Cells Using Surface-Enhanced Raman Spectroscopy (SERS)

Structural changes and chemical modifications in DNA during interactions with X-ray radiation are still not clear within 48 h of incubation. We investigate genomic DNA from the radiated CNE2 cell line within 48 h of incubation using surface-enhanced Raman spectroscopy (SERS). Multivariate methods including principal component analysis (PCA) and random forest are proposed to explore the statistical significance before and after radiation. Our results show that intensities of several bands change after radiation, which indicates backbone damage and base-unstacking. Biological effects from DNA damage repairing process may be simultaneously stimulated and different from incubation time. Under doses of 10 Gy (with 24 and 48 h of incubation) and 20 Gy (with 48 h of incubation), the relative contents of C against T and A against G deviate obviously from the control level. Statistical results strengthen significantly the idea that modification in DNA bases is associated with the disruption of base-stacking in the DNA duplex. Our findings provide vital information for radiation-induced the DNA damage at the molecular level, which may provide insight into the effect and mechanism of anticarcinogens in tumor therapy.

Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study

In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm⁻¹. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm⁻¹ of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG) and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA), eight different grapevine varieties were discriminated.

Fast Optical Chemical and Structural Classification of RNA

As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs.

Hierarchical Plasmonic Nanorods and Upconversion Core-Satellite Nanoassemblies for Multimodal Imaging-Guided Combination Phototherapy

DNA-driven hierarchical core-satellite nanostructures with plasmonic gold nanorod dimers and upconversion nanoparticles are fabricated. Once the core-satellite structure is activated, combined photothermal therapy and photodynamic therapy are carried out under the guidance of upconversion luminesce, T1 -weighted magnetic resonance, photoacoustics, and computed tomography imaging of tumors in vivo, which exhibit the multifunctional biological applications of the DNA-based self-assemblies.

Nanostructured SERS-electrochemical biosensors for testing of anticancer drug interactions with DNA

Widely used anti-cancer treatments involving chemotherapeutic drugs result in cancer cell damage due to their strong interaction with DNA. In this work, we have developed laboratory biosensors for screening chemotherapeutic drugs and to aid in the assessment of DNA modification/damage caused by these drugs. The sensors utilize surface-enhanced Raman scattering (SERS) spectroscopy and electrochemical methods to monitor sensory film modification and observe the drug-DNA reactivity. The self-assembled monolayer protected gold-disk electrode (AuDE) was coated with a reduced graphene oxide (rGO), decorated with plasmonic gold-coated Fe2Ni@Au magnetic nanoparticles functionalized with double-stranded DNA (dsDNA), a sequence of the breast cancer gene BRCA1. The nanobiosensors AuDE/SAM/rGO/Fe2Ni@Au/dsDNA were then subjected to the action of a model chemotherapeutic drug, doxorubicin (DOX), to assess the DNA modification and its dose dependence. The designed novel nanobiosensors offer SERS/electrochemical transduction, enabling chemically specific and highly sensitive analytical signals generation. The SERS measurements have corroborated the DOX intercalation into the DNA duplex whereas the electrochemical scans have indicated that the DNA modification by DOX proceeds in a concentration dependent manner, with limit of detection LOD=8 µg/mL (S/N=3), with semilog linearity over 3 orders of magnitude. These new biosensors are sensitive to agents that interact with DNA and facilitate the analysis of functional groups for determination of the binding mode. The proposed nanobiosensors can be applied in the first stage of the drug development for testing the interactions of new drugs with DNA before the drug efficacy can be assessed in more expensive testing in vitro and in vivo.

Silver colloids as plasmonic substrates for direct label-free surface-enhanced Raman scattering analysis of DNA

Unraveling the role played by the surface chemistry of silver colloids in the direct SERS analysis of DNA.

Photonic Crystal Hydrogel Enhanced Plasmonic Staining for Multiplexed Protein Analysis

Plasmonic nanoparticles are commonly used as optical transducers in sensing applications. The optical signals resulting from the interaction of analytes and plamsonic nanoparticles are influenced by surrounding physical structures where the nanoparticles are located. This paper proposes inverse opal photonic crystal hydrogel as 3D structure to improve Raman signals from plasmonic staining. By hybridization of the plasmonic nanoparticles and photonic crystal, surface-enhanced Raman spectroscopy (SERS) analysis of multiplexed protein is realized. It benefits the Raman analysis by providing high-density "hot spots" in 3D and extra enhancement of local electromagnetic field at the band edge of PhC with periodic refractive index distribution. The strong interaction of light and the hybrid 3D nanostructure offers new insights into plasmonic nanoparticle applications and biosensor design.

Biomarker detection technologies and future directions

Biomarkers play a vital role in disease detection and treatment follow-up. It is important to note that diseases in the early stage are typically treated with the greatest probability of success. However, due to various technical difficulties in current technologies for the detection of biomarkers, the potential of biomarkers is not explored completely. Therefore, the developments of technologies, which can enable the accurate detection of prostate cancer at an early stage with simple, experimental protocols are highly inevitable. This critical review evaluates the current methods and technologies used in the detection of biomarkers. The aim of this article is to provide a comprehensive review covering the advantages and disadvantages of the biomarker detection methods. Future directions for the development of technologies to achieve highly selective and sensitive detection of biomarkers for point-of-care applications are also commented on.

Elucidation of ultraviolet radiation-induced cell responses and intracellular biomolecular dynamics in mammalian cells using surface-enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy has been used to elucidate biomolecular dynamics on the response of mammalian cells towards UV light irradiation.

Fingerprinting biochemical changes associated with cellular responses to external stimuli can provide vital information on the dynamics of biological processes and their defense mechanisms. In this study, surface-enhanced Raman spectroscopy (SERS) has been used to elucidate biomolecular dynamics on the response of healthy and cancerous cells towards ultraviolet (UV) light irradiation at the cellular level in real-time. We have identified a number of physiochemical damages to proteins, especially to the chemical structure of the sulfur and aromatic amino acid containing moieties, as well as changes in secondary structure. Furthermore, we found that continuous exposure of short wave UV-C light (254 nm) to living cells can photolytically damage intracellular proteins and can completely arrest nanoparticle transport and trigger apoptosis. However, under similar conditions, this was not observed when the cells were exposed to long wave UV-A light (365 nm). These biomolecular events were probed in real-time using SERS and dark-field (DF) imaging. Specifically, this technique has been utilized for the real-time evaluation of a unique cellular defense mechanism in cancer cells towards UV exposure. Our technique provides a powerful approach to understand the mechanisms of UV light-triggered cell death, protein dynamics, and enhanced cell repair and defense machinery within cancer cells through actively monitoring molecular vibrations.

Bio-Conjugated Gold Nanoparticle Based SERS Probe for Ultrasensitive Identification of Mosquito-Borne Viruses Using Raman Fingerprinting

Dengue virus (DENV) and West Nile virus (WNV) are two well-documented mosquito-borne flaviviruses that cause significant health problems worldwide. Driven by this need, we have developed a bio-conjugated gold nanoparticle (AuNP)-based surface enhanced Raman spectroscopy (SERS) probe for the detection of both DENV and WNV. Reported data demonstrate anti-flavivirus 4G2 antibody conjugated gold nanoparticle (GNP) SERS probe can be used as a Raman fingerprint for the ultrasensitive detection of DENV and WNV selectively. Experimental data show that due to the plasmon coupling in nano-assembly, antibody conjugated GNP- based SERS is able to detect as low as 10 plaque-forming units (PFU)/ml of DENV-2 and WNV, which is comparable with the sensitivity of quantitative PCR-based assays. Selectivity of our probe was demonstrated using another mosquito-borne chikungunya virus (CHIKV) as a negative control. Experimental data demonstrate a huge enhancement of SERS intensity is mainly due to the strong electric field enhancement, which has been confirmed by the finite-difference time-domain (FDTD) simulation. Reported FDTD simulation data indicate the SERS enhancement factor can be more than 10⁴ times, due to the assembled structure. Reported results suggest that bio-conjugated AuNP-4G2 based SERS probes have great potential to be used to screen viral particles in clinical and research-based laboratories.

Aptamer-conjugated theranostic hybrid graphene oxide with highly selective biosensing and combined therapy capability

Cancer is a life-threatening disease, which is rapidly becoming a global pandemic. Driven by this need, here we report for the first time an aptamer-conjugated theranostic magnetic hybrid graphene oxide-based assay for highly sensitive tumor cell detection from blood samples with combined therapy capability. AGE-aptamer-conjugated theranostic magnetic nanoparticle-attached hybrid graphene oxide was developed for highly selective detection of tumor cells from infected blood samples. Experimental data indicate that hybrid graphene can be used as a multicolor luminescence platform for selective imaging of G361 human malignant melanoma cancer cells. The reported results have also shown that indocyanine green (ICG)-bound AGE-aptamer-attached hybrid graphene oxide is capable of combined synergistic photothermal and photodynamic treatment of cancer. Targeted combined therapeutic treatment using 785 nm near-infrared (NIR) light indicates that the multimodal therapeutic treatment is highly effective for malignant melanoma cancer therapy. The reported data show that this aptamer-conjugated theranostic graphene oxide-based assay has exciting potential for improving cancer diagnosis and treatment.

Quantitative SERS-based DNA detection assisted by magnetic microspheres

We report a quantitative SERS measurement scheme based on the magnetic microsphere–Ag nanoparticles to detect target DNA.